List of problems reported in CheckMyMetal

DATE OF BUG REPORT BUG EXPLANATION QUERY TYPE STATUS FIXED AT
March 10, 2024 6bjr does not show bug Not fixed None
Feb. 15, 2024 5j4d 500 error bug Not fixed None
Jan. 23, 2024 6xwz does not center well bug Not fixed None
Jan. 12, 2024 get Server Error (500) no matter what I submit. bug Fixed Jan. 23, 2024
Jan. 7, 2024 I upload my PDB file but I get a served 500 error right after submitting my job. What should I do? bug Fixed Jan. 23, 2024
Nov. 3, 2023 7XK6 should show Ca ion, prolem with NH, changing xyz coordinates of ions helps but why? bug Not fixed None
Nov. 3, 2023 Add validations of halogens: 8AD0 bug Not fixed None
Aug. 24, 2023 It seems like almost all metals in all pdb files now give very poor scores, 6 or lower, even ones that performed much better a week ago. Dear User, Thank you for providing your feedback. In comparing metal ions, an approximate ranking can be established by considering the metal in the position of the current one. This comparison involves three parameters that may vary: Atomic contacts Valence Geometry Each of these parameters contributes a maximum of 2 points, resulting in a total potential score of 6 in the current version. In previous versions, the remaining parameters were remaining constant. E.g. Parameters such as B-factor (env) are not taken into consideration due to the requirement of approximately 3 cycles of refinement for each metal ion to attain accurate results. Such process would demand a significant amount of time. We can implement choosing scooring approach (old/new) in upcoming ~2 weeks. Best regards, Minor Lab bug Partially fixed Aug. 26, 2023
May 24, 2023 cmm soes not draw distances to sulfurs bug Fixed Aug. 24, 2023
May 20, 2023 3wax doe snot work bug Not fixed None
April 13, 2023 fix pymol_select line 94 bug Not fixed None
Feb. 7, 2023 In the pdb 1IHH, the platinum center is correctly assigned having the oxidation state (II) and a square planar geometry. However the geometry field is highlighted in yellow, which I do not understand. See also (4) Kuppuraj G, Dudev M, Lim C (2009) J. Phys. Chem. B, 113, 2952-2960. Thanks for checking! Best regards Bernhard bug Fixed Aug. 22, 2023
Jan. 26, 2023 Distances when using cif file are not shown bug Not fixed None
Nov. 21, 2022 8EW4 shows wrong diff map bug Not fixed None
Nov. 18, 2022 Zn square plannar is now in both version as dubious suggestion Fixed Nov. 18, 2022
Nov. 15, 2022 Install pymol module in django version bug Fixed Nov. 18, 2022
Nov. 4, 2022 precalculated dirs should be deleted if there is modification to display fresh ones suggestion Not implemented None
Nov. 3, 2022 1a2p contact.pdb file is not generetaed (listsite route) bug Fixed Nov. 3, 2022
Oct. 24, 2022 add diffrences during ref to Fe(III) and Fe(II) bug Not fixed None
Oct. 17, 2022 /home/michal_g/Documents/cmm/fix1/pdb.cif does not work bug Not fixed None
Oct. 17, 2022 if DELFWT PHDELWT and FOFCWT PHFOFCWT do it in pairs not mix bug Not fixed None
Oct. 17, 2022 write new faster neighborhood bug Not fixed None
Oct. 14, 2022 7LVK don't work bug Not fixed None
Oct. 13, 2022 Change acceptable (upload) to automatically used suggestion Not implemented None
Sept. 30, 2022 Update REFMAC version, please. suggestion Not implemented None
Sept. 27, 2022 4ab2 dows not work bug Not fixed None
Sept. 23, 2022 1ppx in cif format does not work (NH does not work) bug Not fixed None
Sept. 23, 2022 test 1ppx on cif if correct distances question Not fixed None
Sept. 22, 2022 Refine pipline should have option to refine with anomalous signal suggestion Not implemented None
Sept. 22, 2022 Brief description of CMM parameters, change ligand to atomic contacts bug Fixed Sept. 23, 2022
Sept. 22, 2022 Do description that right now mtz can produce maps suggestion Implemented Sept. 22, 2022
Sept. 22, 2022 Maps are now generated from mtz. Uploading mtz file is now enough to generate maps. suggestion Implemented Sept. 22, 2022
Sept. 22, 2022 2fna shows two sites at once bug Fixed Sept. 23, 2022
Sept. 22, 2022 Inform that after substitution withour ref maps are old and b fact also suggestion Not implemented None
Sept. 21, 2022 CHnge acceptable -sf.cif to .cif bug Fixed Sept. 26, 2022
Sept. 19, 2022 4MDG is listing only 2 sites out of 11. bug Not fixed None
Sept. 19, 2022 4p3q does not work bug Not fixed None
Sept. 19, 2022 Display only model 0/1 1PPX bug Fixed Sept. 23, 2022
Sept. 19, 2022 Show only bonds for N/O not C bug Fixed Sept. 23, 2022
Sept. 19, 2022 When no mtz/-sf.cif hide the list of ref bug Fixed Sept. 26, 2022
Sept. 13, 2022 Report bug is not working on validation page bug Fixed Sept. 14, 2022
Sept. 13, 2022 Maps should be available if an MTZ file is submitted. Maps should not have to be uploaded. suggestion Implemented Jan. 24, 2023
Feb. 18, 2022 Toggle spin with button instead of checkbox suggestion Fixed None
Feb. 11, 2022 time out 504, fix apache config file bug Fixed Feb. 11, 2022
Jan. 13, 2022 4ins.cif problem debug errors bug Fixed Sept. 19, 2022
Jan. 13, 2022 cif format does not produce neeighbor unit atoms suggestion Not implemented None
Jan. 13, 2022 pdb format does not produce neeighbor unit atoms bug Fixed Jan. 13, 2022
Jan. 7, 2022 showing statistics on homepage bug Fixed Jan. 7, 2022
Dec. 21, 2021 5t6l strange name of residues bug Fixed Sept. 19, 2022
Dec. 16, 2021 site is crushed when pdb have no metals bug Fixed Dec. 17, 2021
Dec. 16, 2021 funcion model_pdb only can do pdb not cif files, review it bug Fixed None
Dec. 16, 2021 refmac works only for residues 801, and it should work on A:801 bug Fixed Dec. 17, 2021
Dec. 15, 2021 CMM does not read crystallization conditions from cif file. bug Fixed Dec. 15, 2021
Dec. 15, 2021 CMM needs also to read mtz file not only -sf.cif. bug Fixed Dec. 17, 2021